run

Command-line tool subcommand

Main command for executing Pimlico modules from the command line run command.

Usage:

pimlico.sh [...] run [modules [modules ...]] [-h] [--force-rerun] [--all-deps] [--all] [--dry-run] [--step] [--preliminary] [--exit-on-error] [--email {modend,end}] [--last-error]

Positional arguments

Arg Description
[modules [modules ...]] The name (or number) of the module to run. To run a stage from a multi-stage module, use ‘module:stage’. Use ‘status’ command to see available modules. Use ‘module:?’ or ‘module:help’ to list available stages. If not given, defaults to next incomplete module that has all its inputs ready. You may give multiple modules, in which case they will be executed in the order specified

Options

Option Description
--force-rerun, -f Force running the module(s), even if it’s already been run to completion
--all-deps, -a If the given module(s) has dependent modules that have not been completed, executed them first. This allows you to specify a module late in the pipeline and execute the full pipeline leading to that point
--all Run all currently unexecuted modules that have their inputs ready, or will have by the time previous modules are run. (List of modules will be ignored)
--dry-run, --dry, --check Perform all pre-execution checks, but don’t actually run the module(s)
--step Enabled super-verbose debugging mode, which steps through a module’s processing outputting a lot of information and allowing you to control the output as it goes. Useful for working out what’s going on inside a module if it’s mysteriously not producing the output you expected
--preliminary, --pre Perform a preliminary run of any modules that take multiple datasets into one of their inputs. This means that we will run the module even if not all the datasets are yet available (but at least one is) and mark it as preliminarily completed
--exit-on-error If an error is encountered while executing a module that causes the whole module execution to fail, output the error and exit. By default, Pimlico will send error output to a file (or print it in debug mode) and continue to execute the next module that can be executed, if any
--email Send email notifications when processing is complete, including information about the outcome. Choose from: ‘modend’ (send notification after module execution if it fails and a summary at the end of everything), ‘end’ (send only the final summary). Email sending must be configured: see ‘email’ command to test
--last-error, -e Don’t execute, just output the error log from the last execution of the given module(s)